In the last 2 decades, both humans and domestic cats have become new hosts for lentivirus. Infection results in progressive immunodeficiency and death in both hosts. In contrast to the disease induced by a lentivirus in a new host species, infection of many feline and primate species is apparently apathogenic, presumably because of a long history of co-adaptation between virus and host. There has been very little research on virus and host factors that lead to apathogenic outcomes of animals naturally infected with lentiviruses. Knowledge of mechanisms that lead to apathogenic, endemic lentivirus infections will provide an essential framework to investigate the pathogenesis and evolution of epidemic lentivirus infections. In order to develop an understanding of endemic feline lentiviruses, we have investigated the epidemiology and molecular evolution of a species-specific feline lentivirus (FIVFco) in wild cougars (Fells concolor) in the western United States. The seroprevalence of FIVFco exceeds 50% in most populations, virus populations evolve at 1.5%/decade, and there is selection against change of viral structural proteins. To further advance this important model, we will initiate studies to discern potential viral mechanisms for a pathogenic infection of FIVFco. We reason that because accessory genes control virus replication and virus-host cell interactions, the arrangement, expression patterns, or function of lentiviral regulatory genes may differ between FIV and FIVFco. In this proposal we will test the hypothesis that the genomic structure of pathogenic FIV and a pathogenic FIVFco will differ in the organization of accessory genes. To address this hypothesis, we will isolate FIVFco genomes that are representative of diverse lineages that we have identified in infected western US cougars, sequence the entire genome, determine genomic organization of FIVfco and compare the genomes of FIVfco and FIV The Specific Aims of the proposal are: Specific Aim 1. To isolate cougar lentiviruses from naturally infected animals; Specific Aim 2. To determine the genomic organization of FIVfco from culture supernatants and tissue DNA; Specific Aim 3. To mentor students in infectious disease research.